Israeli authorities have raided the offices of multiple Palestinian advocacy and aid groups that it says are terror organisations.

Two of the groups say the IDF used iron plates to seal the entrances to their Ramallah premises and left notices that declared them closed.

Israel has alleged that the groups have been operating as arms of the Popular Front for the Liberation of Palestine, a US and EU-designated terror organisation.

The groups have rejected claims they are linked to the PFLP and have accused Israel of attempting to stifle criticism of alleged human rights issues.

Last October six Palestinian advocacy groups: Addameer, al-Haq, Bisan Center for Research and Development, Defence for Children International – Palestine, the Union of Agricultural Work Committees, and the Union of Palestinian Women's Committees, were designated as terror groups by the Israeli government who alleged their links with the PLFP.

On Wednesday night, Israeli Defence Minister Benny Gantz ratified these designations. He accused the groups of having known terrorists on their payrolls despite them not being employed by them.

The same day the chief of the IDF’s Central Command rejected appeals by al-Haq, and Defense for Children-International in Palestine to be taken off the terror list.

In a statement released on Thursday morning, the IDF announced that troops had shuttered the offices of seven organisations in the West Bank overnight, and admitted to confiscating “property belonging to the terror organisations.”

The IDF also added: “During the counterterrorism activity, rocks and Molotov cocktails were hurled toward the soldiers, who responded with riot dispersal means.”

“They came, blew up the door, got inside, and messed with the files,” al-Haq director Shawan Jabarin told  The Associated Press, but said they were still checking whether the troops had taken any documents.

The UN Human Rights Office has said the raids “appear totally arbitrary”, claiming Israel did not provide sufficient evidence that the NGOs' are linked to terror.

Last October’s declaration sparked international criticism from a range of governments and groups. 

This July nine EU members accused Israel of providing no evidence to justify linking the groups to terror and vowed to continue funding them.

The majority of the targeted organisations document alleged human rights violations by both Israel and Palestinian Authority, which regularly detain Palestinian activists. EU member states and the UN are among the donors for many of them.

Jabarin said that “neighbours and strangers” close to al-Haq’s Ramallah office on Thursday had re-opened the premises once Israeli forces had gone and that the group’s staff had resumed their work inside the building.

“We don’t take permission from any Israeli military or political official. We are proceeding, encouraged by our belief in accountability and the international law,” he went on.

The PA slammed the raids as “an attempt to silence the voice of truth and justice.” 

Yesh Din, an Israeli NGO that says it advocates “structural, long-term improvement to human rights in the Occupied Palestinian Territories”, said Thursday’s raid should “worry anyone who values ​​human rights.

They also, “called on the countries of the world to intervene in order to stop Israel’s political persecution against Palestinian human rights organisations, which is intended to justify the continuation of the crimes of occupation and apartheid in the West Bank”.

The Defence Ministry has accused the recently raided groups of “operating undercover for the PFLP,” and argued that they work “under the guise of performing humanitarian activities.”

“The organisations operate to strengthen the organisation and to recruit operatives. They also assist in raising funds for the terror organisation via a variety of methods that include forgery and fraud,” concealing their terror affiliations “out of fear” of Israeli and other international security agencies.

NGO Monitor, the Israel-based nonprofit that said it works to end the promotion of "politically and ideologically motivated anti-Israel agendas", argued that Gantz’s latest ratification was “a response to the European refusal to engage with the evidence.”

“Even without any classified intelligence, open source information published by NGO Monitor clearly shows the links between the PFLP and the European funded NGOs,” claimed the nonprofit’s founder Gerald Steinberg.

Under Israeli military and civil law, support or membership of a terror group is illegal and can result in jail sentences.

Last May the Israeli security agency Shin Bet arrested four suspects it said had funnelled European funds into the PFLP.